Page contents:

On this page, you can find R/Bioconductor libraries for Unix/Linux
and Windows:
1. Bioconductor support libraries for the human and mouse NuGO
arrays.
2. Bioconductor annotation libraries for the Affymetrix Gene Titan
system that are not provided by the Bioconductor project.
3. Bioconductor CDF libraries for the Affymetrix gene ST arrays and
Gene Titan System that are not provided by the Bioconductor project.
4. Bioconductor pdInfo files for the Affymetrix gene ST arrays and
Gene Titan System that are not provided by the Bioconductor project.
5. Bioconductor libraries for the MBNI
Custom Chip Definition Files (CDFs) for the human and mouse NuGO
arrays (cdf, probe, and Entrez gene annotation).
6. For the current MBNI
Custom Chip Definition Files (CDFs) release: Bioconductor libraries
for human, mouse, and rat species that we support (Entrez gene; also
probe and cdf)*.

*: For
convenience, we mirror the probe and CDF files as provided by MBNI.
The version 19.0.2 annotation libraries are created by ourselves. We
provide only the Entrezg .db-libraries, and .db-tairg libraries for
Arabidopsis.

REMARK:
we decided to use the ENTREZ Custom CDF-files for the following
reasons:

Most up-to-date.

Corresponds to genes (not transcripts).

Accepted input for follow-up analyses.

Off course, you are free to use one of the other formats, e.g.
ENSEMBL, but we do not provide Bioconductor annotation libraries for
those custom CDFs.

hs: human microarrays; mm: mouse microarrays, and YES: these
libraries are officially supported via Bioconductor!
Now, support for the oligo library (the pd.nugo.* packages) is also
provided.

Custom CDFs:Please do this if you receive an error message on missing
libraries (only the lacking libraries need to be installed):
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("org.At.tair.db", "org.Hs.eg.db",
"org.Mm.eg.db", "org.Rn.eg.db"))

Current Custom CDF is version 19.0.0 (Nov 33, 2014). If new Custom
CDF libraries are released, the version will shift up (and the
current repository will be dropped).
Please check the tables below to see whether your chip is supported!
Simply use the proper library names in the commands as shown in the
examples above.

Manual Installation

Installation instructions

For Windows: download the appropriate .zip-files from the tables
below. In RGui, go to Packages => Install package(s) from local
zip-files... Browse to the location where you downloaded your
.zip-files and select the files you want to install. Done!

For Unix/Linux: download the appropriate .tar.gz files from the
tables below. cd to the directory where you downloaded your .tar.gz
files and execute the following command (multiple times for multiple
.tar.gz files): R CMD INSTALL <your downloaded .tar.gz file>.

Patched Affy-library

Affy no longer supports loading Gene ST 2.0 arrays. Please use
the patched affy-library if you really want to do this.NOTE: using the patched affy-library is for your own
risk! Please try the oligo or xps packages instead.

Download tables

1. Human and mouse NuGO array support files. Both the 'affy' and
'oligo' support libraries are present. Note that for 'oligo' only
the pdInfo file is
needed (and that the annotation is lacking). For
'affy' you need to download and install all three libraries for each
chip!

2. Human and mouse NuGO array support files (VERSION
19.0.0; DB VERSION 19.0.2); MBNI
Custom CDF; Nov 13, 2014; DB: November 2015).
To obtain full microarray support, you need to download and install
all three libraries for each chip!

3. Annotation libraries for the
Affymetrix GeneTitan plates (based on the
AFFYMATRIX probe annotations).
Updated November 2015 for Bioconductor 3.2.
The CDF and PROBE libraries are available on http://www.bioconductor.org
or via the biocLite()
command.
To obtain full microarray support, you need to
download and install all three libraries (cdf. probe, and .db) for
each chip!

4. Affymetrix-derived CDF (and
.DB) R-environments AND binary CDFs for the gene ST arrays and the
GeneTitan plates.
Updated November 2015 / Bioconductor 3.2 (binary
files January 2013).
These environments and binary CDFs are created
utilizing Platform Design Info packages (library Oligo).
Please note that these files are "unsupported",
i.e. not generated nor endorsed by Affymetrix, so you agree to use
them on your own risk.

5. Annotation libraries for the MBNI
Custom CDF annotation files (mirrored from MBNI; VERSION
19.0.0
Updated November 2015 / Bioconductor 3.2. Here,
also the CDF and PROBE libraries are available for download.
To obtain full microarray support, you need to
download and install all three libraries for each chip!